Metagenomic Discovery of Biomass-Degrading Genes from Cow Rumen
Background Metagenomic analysis involves the recovery of DNA from environmental samples. This method allows people to look at DNA from a multiple organisms at the same time. The goal of this type of sampling is often to look at microbial communities and how they interact with or have become specialized to deal with the environment around them. Many diverse environments exist where microbes have evolved to deal with the specific challenges presented to them. This presents an opportunity for researchers to study and perhaps mimic how these microbes survive and live in such diverse areas. An interesting microbial community exists within the rumen of cows. Cows and the microbiome within them have evolved to very efficiently consume and process large amounts of cellulosic food. Inside the rumen of cows, a microbial community exists that aids in the degradation of cellulosic biomass. Often many of these microbes resist cultivation so a metagenomic approach is often advantageous. Metagenomic Analysis Researchers at the Department of Energy performed a metagenomic assessment of the microbiome inside of a cow's rumen. Hess, Matthias, et al. "[http://www.sciencemag.org/content/331/6016/463.short Metagenomic discovery of biomass-degrading genes and genomes from cow rumen]." ''Science'' 331.6016 (2011): 463-467. Samples from the cow's rumen were extracted, the microbial DNA was isolated and a genetic library was constructed. They did this so that they could easily manipulate the DNA in the same host. From the rumen samples, the researchers extracted 268 gigbases of genomic information and assembled the sequences via de novo assembly. They then had to predict which genes could potentially produce proteins that would actively interact with carbohydrates. They identified a total of 27,755 genes that could potentially interact with carbohydrates and compared those genes with databases of known carbohydrate interactive genes. Only 5% of the identified genes were more than 75% percent identical to previously identified genes. This means that the study produced a wealth of metagenomic information that had not been previously unidentified about cellulose breakdown and carbohydrate metabolism. In fact, 43% of the genes they identified were less than 50% identical to previously identified genes. Implications Organisms in extreme environments have evolved to have very interesting and diverse characteristics because the selective pressure is so high. These organisms have two choices, either adapt or die. This proves useful for us because oftentimes we are able to take advantage of nature's optimization to build our own synthetic biological networks to work in similar extreme environments. Examples of this include bacteria populations found near oil spills useful for the microbial production of biofuels. Head, Ian M., D. Martin Jones, and Wilfred FM Röling. "[http://www.nature.com/nrmicro/journal/v4/n3/abs/nrmicro1348.html Marine microorganisms make a meal of oil]." ''Nature Reviews Microbiology'' 4.3 (2006): 173-182. Most of the current biofuel producing strains of bacteria find it difficult to survive in environments rich in hydrocarbons, but by studying bacterial populations that survive well in these extreme conditions we can improve our systems. Also, microbes that are found at bioremediation sites can be useful to study to learn more about how the remediation actually takes place. Yergeau, Etienne, et al. "[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030058#pone-0030058-g002 Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils.]" ''PloS one'' 7.1 (2012): e30058. References